08032015155118835m0500
type: Ontology
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> Model Status This version has had a stimulus protocol component added to allow the model to simulate multiple action potentials, has been unit checked and curated and is known to run in COR and PCEnv. <sect1 id="sec_structure"> Model Structure In a series of papers published in 1952, A.L. Hodgkin and A.F. Huxley presented the results of a series of experiments in which they investigated the flow of electric current through the surface membrane of the giant nerve fibre of a squid. In the summary paper of the Hodgkin and Huxley model, the authors developed a mathematical description of the behaviour of the membrane based upon these experiments, which accounts for the conduction and excitation of the fibre. The form of this description has been used as the basis for almost all other ionic current models of excitable tissues, including Purkinje fibres and cardiac atrial and ventricular muscle. The summary paper is cited below: A Quantitative Description of Membrane Current and its Application to Conduction and Excitation in Nerve, A. L. Hodgkin and A. F. Huxley, 1952, The Journal of Physiology , 117, 500-544. PubMed ID: 12991237 <informalfigure float="0" id="fig_circuit_diagram"> <mediaobject> <imageobject> <objectinfo> Electrical circuit describing the current across the cell membrane </objectinfo> <imagedata fileref="hodgkin_1952.png" /> </imageobject> </mediaobject> A schematic cell diagram describing the current flows across the cell membrane that are captured in the Hodgkin Huxley model. </informalfigure> </sect1> </documentation>
has cell m lrdf markup: <rdf:RDF xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:j.0="http://www.cellml.org/bqs/1.0#" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:j.1="http://imc.org/vCard/3.0#" xmlns="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:j.2="http://www.cellml.org/metadata/simulation/1.0#"> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0"> <cmeta:modification> <rdf:Description rdf:about="rdf:#384803b0-d02a-414d-86fe-2ead34d6ede9"> <cmeta:modifier> <rdf:Description rdf:about="rdf:#85f445d5-2b20-4a8a-937a-44890e1ccf00"> <vcard:N> <rdf:Description rdf:about="rdf:#9b923383-f1a8-48c7-b1ee-0ca41c08de54"> <vcard:Given xml:lang="en">David</vcard:Given> <vcard:Family xml:lang="en">Nickerson</vcard:Family> </rdf:Description> </vcard:N> </rdf:Description> </cmeta:modifier> <modified> <rdf:Description rdf:about="rdf:#70448d97-7f25-4048-8bd3-da91d466bfd1"> <W3CDTF xml:lang="en">2002-11-20</W3CDTF> </rdf:Description> </modified> <rdf:value xml:lang="en">Correcting the equation for dv/dt.</rdf:value> </rdf:Description> </cmeta:modification> <cmeta:modification> <rdf:Description rdf:about="rdf:#70de1e12-eccf-4c2c-a514-a53a1018aeb3"> <cmeta:modifier> <rdf:Description rdf:about="rdf:#e897f342-e771-4ae3-876d-062dfdfccc88"> <vcard:N> <rdf:Description rdf:about="rdf:#56197c17-2399-482e-9645-a522ed0beb31"> <vcard:Other xml:lang="en">Richard</vcard:Other> <vcard:Given xml:lang="en">James</vcard:Given> <vcard:Family xml:lang="en">Lawson</vcard:Family> </rdf:Description> </vcard:N> </rdf:Description> </cmeta:modifier> <modified> <rdf:Description rdf:about="rdf:#5bc4f7d2-1306-4281-88b5-a5afe628bc66"> <W3CDTF xml:lang="en">2007-06-15T12:32:55+12:00</W3CDTF> </rdf:Description> </modified> <rdf:value xml:lang="en">Added stimulus protocol to allow simulation of trains of action potentials. The stimulus amplitude (20 microamperes per cm2) and duration (0.5 ms) were taken from the single stim…
legacy code URI: C:\Users\chthompson\Dropbox\Work Related\Annotated Models\Hodgkin_1952\hodgkin_huxley_1952.cellml
annotator name: Christopher Thompson
model id: hodgkin_huxley_squid_axon_1952
model name: hodgkin_huxley_squid_axon_1952

Charge flow rate
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Charge flow rate

Charge amount
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Charge amount

sodium(1+)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: sodium(1+)

potassium(1+)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: potassium(1+)

calcium ion
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: calcium ion

Nerve fiber
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Nerve fiber

Plasma membrane
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Plasma membrane

Composite physical entity
type: Class
subclass of: Physical entity
disjoint with: Custom physical entity
disjoint with: Reference physical entity
comment: A physical entity that is defined by linking multiple physical entity terms with structural relations.

Computation
type: Class
subclass of: Computational model component
disjoint with: Data structure
comment: A mathematical and/or logical expression that determines the value of a data structure.

Computational model component
type: Class
subclass of: SemSim component
disjoint with: Physical model component
comment: An element of a SemSim model that relates to the mathematical or logical representation of physical quantities or qualities.

Custom physical dependency
type: Class
subclass of: Physical dependency
disjoint with: Reference physical dependency
comment: A physical dependency defined in a specific SemSim model.

Custom physical entity
type: Class
subclass of: Physical entity
comment: A physical entity defined in a specific SemSim model.

Custom physical process
type: Class
subclass of: Physical process
comment: A physical process defined in a specific SemSim model.

Custom physical property
type: Class
subclass of: Physical property
disjoint with: Reference physical property
comment: A physical property defined in a specific SemSim model.

Data structure
type: Class
subclass of: Computational model component
comment: A computational element that stores numerical and/or logical information related to the model.

Decimal
type: Class
subclass of: Real
disjoint with: Integer
comment: A data structure whose value is limited to decimals.

Integer
type: Class
subclass of: Real
comment: A data structure whose value is limited to the whole numbers.

MMLchoice
type: Class
subclass of: Real
comment: A data structure unique to JSim's Mathematical Modeling Language (MML) used to set one or more model input values at runtime.

Physical dependency
type: Class
subclass of: Physical model component
disjoint with: Physical entity
disjoint with: Physical process
disjoint with: Physical property
comment: A quantitative relation between values of physical properties that occurs over a span of time and that determines the time-course of a physical process.

Physical entity
type: Class
subclass of: Physical model component
disjoint with: Physical process
disjoint with: Physical property
comment: A physics analytical entity that represents the material, energy, and/or information content of material or immaterial, space-occupying continuants.

Physical model component
type: Class
subclass of: SemSim component
comment: A SemSim model element used to represent, in whole or in part, the physical meaning of a computational element.

Physical process
type: Class
subclass of: Physical model component
disjoint with: Physical property
comment: A physical processural entity that is a flow, or the control of a flow, of energy and/or information amongst physical continuants that are participants in the physical process.

Physical property
type: Class
subclass of: Physical model component
comment: A physical attribute of an instance of a physical entity, an occurrence of a physical process, or a physical dependency that has a quantitative value that is measurable by a physical device or method, or is computable from such values.

Real
type: Class
subclass of: Data structure
comment: A data structure whose value is limited to the real numbers.

Reference physical dependency
type: Class
subclass of: Physical dependency
comment: A physical dependency that is defined using a term in an external knowledge resource.

Reference physical entity
type: Class
subclass of: Physical entity
comment: A physical entity that is defined using a term from an external knowledge resource.

Reference physical process
type: Class
subclass of: Physical process
comment: A physical process that is defined using a term in an external knowledge resource.

Reference physical property
type: Class
subclass of: Physical property
comment: A physical property that is defined using a term in an external knowledge resource.

Relational constraint
type: Class
subclass of: Computational model component
comment: A logical expression that constrains, but does not define, the value of a data structure. Example: x > 0.

SemSim component
type: Class
comment: A computational or physical element of a SemSim model.

Submodel
type: Class
subclass of: Physical model component
comment: A grouping of one or more data structures that comprise a computationally or physically distinct part of a model or submodel.

Unit of measurement
type: Class
subclass of: Computational model component
comment: A physical quantity chosen as a standard in terms of which other physical quantities may be expressed.

sodium(1+)
type: NamedIndividual
refers to: sodium(1+)
is index entity for: CHEBI 29101 part of Nerve fiber
part of: Nerve fiber

potassium(1+)
type: NamedIndividual
refers to: potassium(1+)
is index entity for: CHEBI 29103 part of Nerve fiber
part of: Nerve fiber

potassium(1+)
type: NamedIndividual
refers to: potassium(1+)
is index entity for: CHEBI 29103 part of Cell culture medium
part of: Cell culture medium 0

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Nerve fiber
part of: Nerve fiber

Leak current across plasma membrane
type: NamedIndividual
type: Custom physical process
comment: Charge flow across the plasma membrane
has source: calcium ion
has sink: Cell culture medium 0
has mediator: Plasma membrane
has physical property: Charge flow rate

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: calcium ion
annotated source: Leak current across plasma membrane

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated source: Leak current across plasma membrane
annotated target: Plasma membrane

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: Cell culture medium 0
annotated source: Leak current across plasma membrane

Nerve fiber
type: NamedIndividual
refers to: Nerve fiber
has part: sodium(1+)
has part: potassium(1+)
has part: calcium ion
has part: Plasma membrane

Plasma membrane
type: NamedIndividual
refers to: Plasma membrane
part of: Nerve fiber
is index entity for: Plasma membrane part of Nerve fiber
has physical property: Charge amount

Plasma membrane
type: NamedIndividual
refers to: Plasma membrane
has physical property: Charge amount

Potassium current across plasma membrane
type: NamedIndividual
type: Custom physical process
comment: Potassium current across plasma membrane
has sink: potassium(1+)
has source: potassium(1+)
has mediator: Plasma membrane
has physical property: Charge flow rate

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: potassium(1+)
annotated source: Potassium current across plasma membrane

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated target: Plasma membrane
annotated source: Potassium current across plasma membrane

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: potassium(1+)
annotated source: Potassium current across plasma membrane

Sodium current across plasma membrane
type: NamedIndividual
type: Custom physical process
has sink: sodium(1+)
has source: Cell culture medium 0
has mediator: Plasma membrane
has physical property: Charge flow rate

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: Cell culture medium 0
annotated source: Sodium current across plasma membrane

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated target: Plasma membrane
annotated source: Sodium current across plasma membrane

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: sodium(1+)
annotated source: Sodium current across plasma membrane

UNIT ampere
type: NamedIndividual
type: Unit of measurement
has computational code: ampere
is fundamental unit: true
unit factor for: UNIT microA per cm2

UNIT farad
type: NamedIndividual
type: Unit of measurement
has computational code: farad
is fundamental unit: true
unit factor for: UNIT microF per cm2

UNIT metre
type: NamedIndividual
type: Unit of measurement
has computational code: metre
is fundamental unit: true
unit factor for: UNIT microA per cm2
unit factor for: UNIT microF per cm2
unit factor for: UNIT milliS per cm2

UNIT microA per cm2
type: NamedIndividual
type: Unit of measurement
has computational code: microA_per_cm2
has unit factor: UNIT ampere
has unit factor: UNIT metre
unit for: leakage current.i L
unit for: membrane.i K
unit for: membrane.i L
unit for: membrane.i Na
unit for: membrane.i Stim
unit for: potassium channel.i K
unit for: sodium channel.i Na

Axiom
has unit factor exponent: -2.0
has unit factor prefix: centi
annotated property: hasUnitFactor
annotated target: UNIT metre
annotated source: UNIT microA per cm2

Axiom
has unit factor prefix: micro
annotated property: hasUnitFactor
annotated target: UNIT ampere
annotated source: UNIT microA per cm2

UNIT microF per cm2
type: NamedIndividual
type: Unit of measurement
has computational code: microF_per_cm2
has unit factor: UNIT farad
has unit factor: UNIT metre
unit for: membrane.Cm

Axiom
has unit factor exponent: -2.0
has unit factor prefix: centi
annotated property: hasUnitFactor
annotated target: UNIT metre
annotated source: UNIT microF per cm2

Axiom
has unit factor prefix: micro
annotated property: hasUnitFactor
annotated target: UNIT farad
annotated source: UNIT microF per cm2

UNIT milliS per cm2
type: NamedIndividual
type: Unit of measurement
has computational code: milliS_per_cm2
has unit factor: UNIT metre
has unit factor: UNIT siemens
unit for: leakage current.g L
unit for: potassium channel.g K
unit for: sodium channel.g Na

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT milliS per cm2
annotated target: UNIT siemens

Axiom
has unit factor exponent: -2.0
has unit factor prefix: centi
annotated property: hasUnitFactor
annotated target: UNIT metre
annotated source: UNIT milliS per cm2

UNIT millisecond
type: NamedIndividual
type: Unit of measurement
has computational code: millisecond
has unit factor: UNIT second
unit for: environment.time
unit for: leakage current.time
unit for: membrane.time
unit for: potassium channel.time
unit for: potassium channel n gate.time
unit for: sodium channel.time
unit for: sodium channel h gate.time
unit for: sodium channel m gate.time

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT millisecond
annotated target: UNIT second

UNIT millivolt
type: NamedIndividual
type: Unit of measurement
has computational code: millivolt
has unit factor: UNIT volt
unit for: leakage current.E L
unit for: leakage current.E R
unit for: leakage current.V
unit for: membrane.E R
unit for: membrane.V
unit for: potassium channel.E K
unit for: potassium channel.E R
unit for: potassium channel.V
unit for: potassium channel n gate.V
unit for: sodium channel.E Na
unit for: sodium channel.E R
unit for: sodium channel.V
unit for: sodium channel h gate.V
unit for: sodium channel m gate.V

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT millivolt
annotated target: UNIT volt

UNIT per millisecond
type: NamedIndividual
type: Unit of measurement
has computational code: per_millisecond
has unit factor: UNIT second
unit for: potassium channel n gate.alpha n
unit for: potassium channel n gate.beta n
unit for: sodium channel h gate.alpha h
unit for: sodium channel h gate.beta h
unit for: sodium channel m gate.alpha m
unit for: sodium channel m gate.beta m

Axiom
has unit factor exponent: -1.0
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT per millisecond
annotated target: UNIT second

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
is fundamental unit: true
unit factor for: UNIT millisecond
unit factor for: UNIT per millisecond

UNIT siemens
type: NamedIndividual
type: Unit of measurement
has computational code: siemens
is fundamental unit: true
unit factor for: UNIT milliS per cm2

UNIT volt
type: NamedIndividual
type: Unit of measurement
is fundamental unit: true
has computational code: volt
unit factor for: UNIT millivolt

environment
type: NamedIndividual
type: Submodel
name: environment
has associated data structure: environment.time
has computational component: environment computation

environment.time
type: NamedIndividual
type: Decimal
metadata ID: environment_time
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: environment.time property
mapped to: leakage current.time
mapped to: membrane.time
mapped to: potassium channel.time
mapped to: sodium channel.time

leakage current
type: NamedIndividual
type: Submodel
name: leakage_current
has associated data structure: leakage current.E L
has associated data structure: leakage current.E R
has associated data structure: leakage current.V
has associated data structure: leakage current.g L
has associated data structure: leakage current.i L
has associated data structure: leakage current.time
has computational component: leakage current computation

leakage current.E L
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Ionic leakage equilibrium potential
has unit: UNIT millivolt
is computational component for: leakage current.E L property

leakage current.E R
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Maximum plasma membrane rest potential
has unit: UNIT millivolt
is computational component for: leakage current.E R property

leakage current.V
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Displacement of the membrane potential from its resting value
has unit: UNIT millivolt
is computational component for: Charge amount

Charge amount
type: NamedIndividual
refers to: Charge amount
physical property of: Plasma membrane
has computational component: leakage current.V

leakage current.g L
type: NamedIndividual
type: Decimal
has start value: 0.3
is discrete: false
is solution domain: false
is declared: true
comment: Ionic leak conductance of the plasma membrane
has unit: UNIT milliS per cm2
is computational component for: leakage current.g L property

leakage current.i L
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
metadata ID: leakage_current_i_L
has cell m lpublic interface: out
is declared: true
comment: Leakage current across the plasma membrane
has unit: UNIT microA per cm2
is computational component for: Charge flow rate
mapped to: membrane.i L

Charge flow rate
type: NamedIndividual
refers to: Charge flow rate
physical property of: Leak current across plasma membrane
has computational component: leakage current.i L

leakage current.time
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: leakage current.time property

leakage current computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>E_L</ci> <apply> <plus /> <ci>E_R</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">10.613</cn> </apply> </apply> <apply> <eq /> <ci>i_L</ci> <apply> <times /> <ci>g_L</ci> <apply> <minus /> <ci>V</ci> <ci>E_L</ci> </apply> </apply> </apply>
is computational component for: leakage current

membrane
type: NamedIndividual
type: Submodel
name: membrane
includes submodel: leakage current
has associated data structure: membrane.Cm
has associated data structure: membrane.E R
has associated data structure: membrane.V
has associated data structure: membrane.i K
has associated data structure: membrane.i L
has associated data structure: membrane.i Na
has associated data structure: membrane.i Stim
has associated data structure: membrane.time
has computational component: membrane computation
includes submodel: potassium channel
includes submodel: sodium channel

Axiom
submodel subsumption type: containment
annotated property: includesSubmodel
annotated source: membrane
annotated target: sodium channel

Axiom
submodel subsumption type: containment
annotated property: includesSubmodel
annotated source: membrane
annotated target: potassium channel

Axiom
submodel subsumption type: containment
annotated property: includesSubmodel
annotated target: leakage current
annotated source: membrane

membrane.Cm
type: NamedIndividual
type: Decimal
has start value: 1
is solution domain: false
is discrete: false
is declared: true
comment: Plasma membrane charge capacity
has unit: UNIT microF per cm2
is computational component for: membrane.Cm property

membrane.E R
type: NamedIndividual
type: Decimal
has start value: -75
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Maximum plasma membrane rest potential
has unit: UNIT millivolt
mapped to: leakage current.E R
is computational component for: membrane.E R property
mapped to: potassium channel.E R
mapped to: sodium channel.E R

membrane.V
type: NamedIndividual
type: Decimal
has start value: -75
is discrete: false
is solution domain: false
metadata ID: membrane_V
has cell m lpublic interface: out
is declared: true
comment: Displacement of the membrane potential from its resting value
has unit: UNIT millivolt
mapped to: leakage current.V
is computational component for: Charge amount
mapped to: potassium channel.V
mapped to: sodium channel.V

Charge amount
type: NamedIndividual
refers to: Charge amount
physical property of: Plasma membrane
has computational component: membrane.V

membrane.i K
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Potassium current across the plasma membrane
has unit: UNIT microA per cm2
is computational component for: Charge flow rate

Charge flow rate
type: NamedIndividual
refers to: Charge flow rate
physical property of: Potassium current across plasma membrane
has computational component: membrane.i K

membrane.i L
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Leakage current across the plasma membrane
has unit: UNIT microA per cm2
is computational component for: Charge flow rate

Charge flow rate
type: NamedIndividual
refers to: Charge flow rate
physical property of: Leak current across plasma membrane
has computational component: membrane.i L

membrane.i Na
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Sodium current across the plasma membrane
has unit: UNIT microA per cm2
is computational component for: Charge flow rate

Charge flow rate
type: NamedIndividual
refers to: Charge flow rate
physical property of: Sodium current across plasma membrane
has computational component: membrane.i Na

membrane.i Stim
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Experimental charge stimulus.
has unit: UNIT microA per cm2
is computational component for: membrane.i Stim property

membrane.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: membrane.time property

membrane computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>i_Stim</ci> <piecewise> <piece> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="microA_per_cm2">20</cn> <apply> <and /> <apply> <geq /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millisecond">10</cn> </apply> <apply> <leq /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millisecond">10.5</cn> </apply> </apply> </piece> <otherwise> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="microA_per_cm2">0</cn> </otherwise> </piecewise> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>V</ci> </apply> <apply> <divide /> <apply> <minus /> <apply> <plus /> <apply> <minus /> <ci>i_Stim</ci> </apply> <ci>i_Na</ci> <ci>i_K</ci> <ci>i_L</ci> </apply> </apply> <ci>Cm</ci> </apply> </apply>
is computational component for: membrane

potassium channel
type: NamedIndividual
type: Submodel
name: potassium_channel
has associated data structure: potassium channel.E K
has associated data structure: potassium channel.E R
has associated data structure: potassium channel.V
has associated data structure: potassium channel.g K
has associated data structure: potassium channel.i K
has associated data structure: potassium channel.n
has associated data structure: potassium channel.time
has computational component: potassium channel computation
includes submodel: potassium channel n gate

Axiom
submodel subsumption type: containment
submodel subsumption type: encapsulation
annotated property: includesSubmodel
annotated source: potassium channel
annotated target: potassium channel n gate

potassium channel.E K
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Potassium ion equilibrium potential
has unit: UNIT millivolt
is computational component for: potassium channel.E K property

potassium channel.E R
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Maximum plasma membrane rest potential
has unit: UNIT millivolt
is computational component for: potassium channel.E R property

potassium channel.V
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
has cell m lprivate interface: out
is declared: true
comment: Displacement of the membrane potential from its resting value
has unit: UNIT millivolt
is computational component for: Charge amount
mapped to: potassium channel n gate.V

Charge amount
type: NamedIndividual
refers to: Charge amount
physical property of: Plasma membrane
has computational component: potassium channel.V

potassium channel.g K
type: NamedIndividual
type: Decimal
has start value: 36
is solution domain: false
is discrete: false
is declared: true
comment: Potassium conductance of the cell membrane
has unit: UNIT milliS per cm2
is computational component for: potassium channel.g K property

potassium channel.i K
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
metadata ID: potassium_channel_i_K
is declared: true
comment: Potassium current across the plasma membrane
has unit: UNIT microA per cm2
mapped to: membrane.i K
is computational component for: Charge flow rate

Charge flow rate
type: NamedIndividual
refers to: Charge flow rate
physical property of: Potassium current across plasma membrane
has computational component: potassium channel.i K

potassium channel.n
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lprivate interface: in
is declared: true
comment: Proportion of activating molecules inside of cell
is computational component for: potassium channel.n property

potassium channel.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
has cell m lprivate interface: out
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: potassium channel.time property
mapped to: potassium channel n gate.time

potassium channel computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>E_K</ci> <apply> <minus /> <ci>E_R</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">12</cn> </apply> </apply> <apply> <eq /> <ci>i_K</ci> <apply> <times /> <ci>g_K</ci> <apply> <power /> <ci>n</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">4</cn> </apply> <apply> <minus /> <ci>V</ci> <ci>E_K</ci> </apply> </apply> </apply>
is computational component for: potassium channel

potassium channel n gate
type: NamedIndividual
type: Submodel
name: potassium_channel_n_gate
has associated data structure: potassium channel n gate.V
has associated data structure: potassium channel n gate.alpha n
has associated data structure: potassium channel n gate.beta n
has associated data structure: potassium channel n gate.n
has associated data structure: potassium channel n gate.time
has computational component: potassium channel n gate computation

potassium channel n gate.V
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Displacement of the membrane potential from its resting value
has unit: UNIT millivolt
is computational component for: Charge amount

Charge amount
type: NamedIndividual
refers to: Charge amount
physical property of: Plasma membrane
has computational component: potassium channel n gate.V

potassium channel n gate.alpha n
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: N gate potassium ion transfer constant (out to in)
has unit: UNIT per millisecond
is computational component for: potassium channel n gate.alpha n property

potassium channel n gate.beta n
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: N gate potassium ion transfer constant (in to out)
has unit: UNIT per millisecond
is computational component for: potassium channel n gate.beta n property

potassium channel n gate.n
type: NamedIndividual
type: Decimal
has start value: 0.325
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Proportion of activating molecules inside of cell
mapped to: potassium channel.n
is computational component for: potassium channel n gate.n property

potassium channel n gate.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: potassium channel n gate.time property

potassium channel n gate computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>alpha_n</ci> <apply> <divide /> <apply> <times /> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_millivolt_millisecond">0.01</cn> </apply> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">65</cn> </apply> </apply> <apply> <minus /> <apply> <exp /> <apply> <divide /> <apply> <minus /> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">65</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">10</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> </apply> <apply> <eq /> <ci>beta_n</ci> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_millisecond">0.125</cn> <apply> <exp /> <apply> <divide /> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">75</cn> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">80</cn> </apply> </apply> </apply> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>n</ci> </apply> <apply> <minus /> <apply> <times /> <ci>alpha_n</ci> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>n</ci> </apply> </apply> <apply> <times /> <ci>beta_n</ci> <ci>n</ci> </apply> </apply> </apply>
is computational component for: potassium channel n gate

sodium channel
type: NamedIndividual
type: Submodel
name: sodium_channel
has associated data structure: sodium channel.E Na
has associated data structure: sodium channel.E R
has associated data structure: sodium channel.V
has associated data structure: sodium channel.g Na
has associated data structure: sodium channel.h
has associated data structure: sodium channel.i Na
has associated data structure: sodium channel.m
has associated data structure: sodium channel.time
has computational component: sodium channel computation
includes submodel: sodium channel h gate
includes submodel: sodium channel m gate

Axiom
submodel subsumption type: containment
submodel subsumption type: encapsulation
annotated property: includesSubmodel
annotated source: sodium channel
annotated target: sodium channel h gate

Axiom
submodel subsumption type: containment
submodel subsumption type: encapsulation
annotated property: includesSubmodel
annotated source: sodium channel
annotated target: sodium channel m gate

sodium channel.E Na
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Sodium ion equilibrium potential
has unit: UNIT millivolt
is computational component for: sodium channel.E Na property

sodium channel.E R
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Maximum plasma membrane rest potential
has unit: UNIT millivolt
is computational component for: sodium channel.E R property

sodium channel.V
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
has cell m lprivate interface: out
is declared: true
comment: Displacement of the membrane potential from its resting value
has unit: UNIT millivolt
is computational component for: Charge amount
mapped to: sodium channel h gate.V
mapped to: sodium channel m gate.V

Charge amount
type: NamedIndividual
refers to: Charge amount
physical property of: Plasma membrane
has computational component: sodium channel.V

sodium channel.g Na
type: NamedIndividual
type: Decimal
has start value: 120
is discrete: false
is solution domain: false
is declared: true
comment: Sodium conductance of the plasma membrane
has unit: UNIT milliS per cm2
is computational component for: sodium channel.g Na property

sodium channel.h
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lprivate interface: in
is declared: true
comment: Proportion of activating molecules inside cell
is computational component for: sodium channel.h property

sodium channel.i Na
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
metadata ID: sodium_channel_i_Na
is declared: true
comment: Sodium current across the plasma membrane
has unit: UNIT microA per cm2
mapped to: membrane.i Na
is computational component for: Charge flow rate

Charge flow rate
type: NamedIndividual
refers to: Charge flow rate
physical property of: Sodium current across plasma membrane
has computational component: sodium channel.i Na

sodium channel.m
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lprivate interface: in
is declared: true
comment: Proportion of inactivating molecules inside of cell
is computational component for: sodium channel.m property

sodium channel.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
has cell m lprivate interface: out
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: sodium channel.time property
mapped to: sodium channel h gate.time
mapped to: sodium channel m gate.time

sodium channel computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>E_Na</ci> <apply> <plus /> <ci>E_R</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">115</cn> </apply> </apply> <apply> <eq /> <ci>i_Na</ci> <apply> <times /> <ci>g_Na</ci> <apply> <power /> <ci>m</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">3</cn> </apply> <ci>h</ci> <apply> <minus /> <ci>V</ci> <ci>E_Na</ci> </apply> </apply> </apply>
is computational component for: sodium channel

sodium channel h gate
type: NamedIndividual
type: Submodel
name: sodium_channel_h_gate
has associated data structure: sodium channel h gate.V
has associated data structure: sodium channel h gate.alpha h
has associated data structure: sodium channel h gate.beta h
has associated data structure: sodium channel h gate.h
has associated data structure: sodium channel h gate.time
has computational component: sodium channel h gate computation

sodium channel h gate.V
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Displacement of the membrane potential from its resting value
has unit: UNIT millivolt
is computational component for: Charge amount

Charge amount
type: NamedIndividual
refers to: Charge amount
physical property of: Plasma membrane
has computational component: sodium channel h gate.V

sodium channel h gate.alpha h
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: H gate sodium ion transfer constant (out to in)
has unit: UNIT per millisecond
is computational component for: sodium channel h gate.alpha h property

sodium channel h gate.beta h
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: H gate sodium ion transfer constant (in to out)
has unit: UNIT per millisecond
is computational component for: sodium channel h gate.beta h property

sodium channel h gate.h
type: NamedIndividual
type: Decimal
has start value: 0.6
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Proportion of activating molecules inside cell
mapped to: sodium channel.h
is computational component for: sodium channel h gate.h property

sodium channel h gate.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: sodium channel h gate.time property

sodium channel h gate computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>alpha_h</ci> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_millisecond">0.07</cn> <apply> <exp /> <apply> <divide /> <apply> <minus /> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">75</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">20</cn> </apply> </apply> </apply> </apply> <apply> <eq /> <ci>beta_h</ci> <apply> <divide /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_millisecond">1</cn> <apply> <plus /> <apply> <exp /> <apply> <divide /> <apply> <minus /> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">45</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">10</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>h</ci> </apply> <apply> <minus /> <apply> <times /> <ci>alpha_h</ci> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>h</ci> </apply> </apply> <apply> <times /> <ci>beta_h</ci> <ci>h</ci> </apply> </apply> </apply>
is computational component for: sodium channel h gate

sodium channel m gate
type: NamedIndividual
type: Submodel
name: sodium_channel_m_gate
has associated data structure: sodium channel m gate.V
has associated data structure: sodium channel m gate.alpha m
has associated data structure: sodium channel m gate.beta m
has associated data structure: sodium channel m gate.m
has associated data structure: sodium channel m gate.time
has computational component: sodium channel m gate computation

sodium channel m gate.V
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Displacement of the membrane potential from its resting value
has unit: UNIT millivolt
is computational component for: Charge amount

Charge amount
type: NamedIndividual
refers to: Charge amount
physical property of: Plasma membrane
has computational component: sodium channel m gate.V

sodium channel m gate.alpha m
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: M gate sodium ion transfer constant (out to in)
has unit: UNIT per millisecond
is computational component for: sodium channel m gate.alpha m property

sodium channel m gate.beta m
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: M gate sodium ion transfer constant (in to out)
has unit: UNIT per millisecond
is computational component for: sodium channel m gate.beta m property

sodium channel m gate.m
type: NamedIndividual
type: Decimal
has start value: 0.05
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Proportion of inactivating molecules inside of cell
mapped to: sodium channel.m
is computational component for: sodium channel m gate.m property

sodium channel m gate.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Time Domain
has unit: UNIT millisecond
is computational component for: sodium channel m gate.time property

sodium channel m gate computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>alpha_m</ci> <apply> <divide /> <apply> <times /> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_millivolt_millisecond">0.1</cn> </apply> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">50</cn> </apply> </apply> <apply> <minus /> <apply> <exp /> <apply> <divide /> <apply> <minus /> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">50</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">10</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> </apply> <apply> <eq /> <ci>beta_m</ci> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_millisecond">4</cn> <apply> <exp /> <apply> <divide /> <apply> <minus /> <apply> <plus /> <ci>V</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">75</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="millivolt">18</cn> </apply> </apply> </apply> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>m</ci> </apply> <apply> <minus /> <apply> <times /> <ci>alpha_m</ci> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>m</ci> </apply> </apply> <apply> <times /> <ci>beta_m</ci> <ci>m</ci> </apply> </apply> </apply>
is computational component for: sodium channel m gate